The purpose of this work is to ascertain the numbers of alleles, allele frequencies, and allele frequency differences among American Indian tribes. The genetic systems being typed are the same as those being used currently in our genetic linkage analyses. Approximately 30 individuals from each of 20 tribes, collected primarily at the Albuquerque Indian Hospital between the years 1992 and 1994, are being analyzed. Various tests for allele frequency differences between tribal groupings based on cultural and linguistic affinities are being performed. This information is important to genetic linkage and disease association studies on Americans Indians because poor estimates of allele frequencies can result in false evidence for linkage and allelic heterogeneity among groups can create spurious associations with disease. In order to more fully quantify isolate structure and exploit such populations for linkage analyses, we have developed a maximum likelihood method to characterize populations by their levels of gene identity. We have applied this method to microsatellite typings for three American Indian and three European populations. Low gene identity was also observed in Europeans (approximately 28%). By contrast, gene identity was higher in all American Indian populations (39%). We also find that while the overall level of gene identity does not vary much between tribes, there are significant differences in allele frequencies. In comparisons among Southwestern American Indians, we find that genetic affiliations are based on geographic proximity, rather than culture or language groupings. Because of the inter-tribal differences in allele frequencies, it is important that linkage analysis in American Indians proceeds with allele frequencies specific for the tribe from which the pedigrees were sampled.